Starting phenix.real_space_refine on Wed Mar 20 16:37:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yn0_33949/03_2024/7yn0_33949.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yn0_33949/03_2024/7yn0_33949.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yn0_33949/03_2024/7yn0_33949.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yn0_33949/03_2024/7yn0_33949.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yn0_33949/03_2024/7yn0_33949.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yn0_33949/03_2024/7yn0_33949.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.006 sd= 0.150 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 153 5.16 5 C 17682 2.51 5 N 4521 2.21 5 O 5556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1148": "OE1" <-> "OE2" Residue "B TYR 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1148": "OE1" <-> "OE2" Residue "C TYR 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1148": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 27912 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 9020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1166, 9020 Classifications: {'peptide': 1166} Link IDs: {'PTRANS': 57, 'TRANS': 1108} Chain breaks: 5 Chain: "B" Number of atoms: 9020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1166, 9020 Classifications: {'peptide': 1166} Link IDs: {'PTRANS': 57, 'TRANS': 1108} Chain breaks: 5 Chain: "C" Number of atoms: 9020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1166, 9020 Classifications: {'peptide': 1166} Link IDs: {'PTRANS': 57, 'TRANS': 1108} Chain breaks: 5 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 15.47, per 1000 atoms: 0.55 Number of scatterers: 27912 At special positions: 0 Unit cell: (155.1, 145.2, 156.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 153 16.00 O 5556 8.00 N 4521 7.00 C 17682 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 195 " distance=2.03 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 214 " distance=2.03 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS A 407 " distance=2.03 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS A 478 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 585 " distance=2.03 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 526 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 654 " distance=2.03 Simple disulfide: pdb=" SG CYS A 620 " - pdb=" SG CYS A 650 " distance=2.03 Simple disulfide: pdb=" SG CYS A 679 " - pdb=" SG CYS A 713 " distance=2.03 Simple disulfide: pdb=" SG CYS A 727 " - pdb=" SG CYS A 736 " distance=2.03 Simple disulfide: pdb=" SG CYS A 806 " - pdb=" SG CYS A 828 " distance=2.03 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=2.03 Simple disulfide: pdb=" SG CYS A 912 " - pdb=" SG CYS A 925 " distance=2.03 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.03 Simple disulfide: pdb=" SG CYS A1156 " - pdb=" SG CYS A1164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 214 " distance=2.03 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS B 407 " distance=2.03 Simple disulfide: pdb=" SG CYS B 425 " - pdb=" SG CYS B 478 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 585 " distance=2.03 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 526 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 654 " distance=2.03 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 650 " distance=2.03 Simple disulfide: pdb=" SG CYS B 679 " - pdb=" SG CYS B 713 " distance=2.03 Simple disulfide: pdb=" SG CYS B 727 " - pdb=" SG CYS B 736 " distance=2.03 Simple disulfide: pdb=" SG CYS B 806 " - pdb=" SG CYS B 828 " distance=2.03 Simple disulfide: pdb=" SG CYS B 811 " - pdb=" SG CYS B 817 " distance=2.03 Simple disulfide: pdb=" SG CYS B 912 " - pdb=" SG CYS B 925 " distance=2.03 Simple disulfide: pdb=" SG CYS B1106 " - pdb=" SG CYS B1117 " distance=2.03 Simple disulfide: pdb=" SG CYS B1156 " - pdb=" SG CYS B1164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 237 " distance=2.03 Simple disulfide: pdb=" SG CYS C 383 " - pdb=" SG CYS C 407 " distance=2.03 Simple disulfide: pdb=" SG CYS C 425 " - pdb=" SG CYS C 478 " distance=2.03 Simple disulfide: pdb=" SG CYS C 437 " - pdb=" SG CYS C 585 " distance=2.03 Simple disulfide: pdb=" SG CYS C 503 " - pdb=" SG CYS C 526 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 654 " distance=2.03 Simple disulfide: pdb=" SG CYS C 620 " - pdb=" SG CYS C 650 " distance=2.03 Simple disulfide: pdb=" SG CYS C 679 " - pdb=" SG CYS C 713 " distance=2.03 Simple disulfide: pdb=" SG CYS C 727 " - pdb=" SG CYS C 736 " distance=2.03 Simple disulfide: pdb=" SG CYS C 806 " - pdb=" SG CYS C 828 " distance=2.03 Simple disulfide: pdb=" SG CYS C 811 " - pdb=" SG CYS C 817 " distance=2.03 Simple disulfide: pdb=" SG CYS C 912 " - pdb=" SG CYS C 925 " distance=2.03 Simple disulfide: pdb=" SG CYS C1106 " - pdb=" SG CYS C1117 " distance=2.03 Simple disulfide: pdb=" SG CYS C1156 " - pdb=" SG CYS C1164 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-6 " BMA E 3 " - " MAN E 4 " " BMA M 3 " - " MAN M 4 " " BMA O 3 " - " MAN O 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " BETA1-6 " NAG F 1 " - " FUC F 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG J 1 " - " FUC J 3 " " NAG R 1 " - " FUC R 3 " NAG-ASN " NAG A1401 " - " ASN A 104 " " NAG A1402 " - " ASN A 166 " " NAG A1403 " - " ASN A 236 " " NAG A1404 " - " ASN A 244 " " NAG A1405 " - " ASN A 619 " " NAG A1406 " - " ASN A 774 " " NAG A1407 " - " ASN A 785 " " NAG A1408 " - " ASN A1176 " " NAG B1401 " - " ASN B1176 " " NAG B1402 " - " ASN B 619 " " NAG B1403 " - " ASN B 774 " " NAG B1404 " - " ASN B 236 " " NAG B1405 " - " ASN B 785 " " NAG B1406 " - " ASN B 166 " " NAG B1407 " - " ASN B 244 " " NAG B1408 " - " ASN B 104 " " NAG C1401 " - " ASN C 236 " " NAG C1402 " - " ASN C 104 " " NAG C1403 " - " ASN C1176 " " NAG C1404 " - " ASN C 166 " " NAG C1405 " - " ASN C 619 " " NAG C1406 " - " ASN C 785 " " NAG C1407 " - " ASN C 774 " " NAG C1408 " - " ASN C 244 " " NAG D 1 " - " ASN A 66 " " NAG E 1 " - " ASN A 222 " " NAG F 1 " - " ASN A 719 " " NAG G 1 " - " ASN A 870 " " NAG H 1 " - " ASN A1213 " " NAG I 1 " - " ASN B 66 " " NAG J 1 " - " ASN B 719 " " NAG K 1 " - " ASN B 870 " " NAG L 1 " - " ASN B1213 " " NAG M 1 " - " ASN B 222 " " NAG N 1 " - " ASN C1213 " " NAG O 1 " - " ASN C 222 " " NAG P 1 " - " ASN C 870 " " NAG Q 1 " - " ASN C 66 " " NAG R 1 " - " ASN C 719 " Time building additional restraints: 11.82 Conformation dependent library (CDL) restraints added in 5.1 seconds 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6510 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 54 sheets defined 26.2% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.05 Creating SS restraints... Processing helix chain 'A' and resid 36 through 41 removed outlier: 3.614A pdb=" N PHE A 40 " --> pdb=" O GLN A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 222 through 230 Processing helix chain 'A' and resid 303 through 307 removed outlier: 3.626A pdb=" N ARG A 307 " --> pdb=" O GLN A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 350 removed outlier: 3.631A pdb=" N GLN A 346 " --> pdb=" O ASN A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 Processing helix chain 'A' and resid 395 through 399 removed outlier: 3.842A pdb=" N PHE A 399 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 415 removed outlier: 4.089A pdb=" N LEU A 414 " --> pdb=" O ASN A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 436 removed outlier: 3.930A pdb=" N SER A 435 " --> pdb=" O ALA A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 457 removed outlier: 4.066A pdb=" N MET A 452 " --> pdb=" O PRO A 449 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N SER A 454 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER A 457 " --> pdb=" O SER A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 524 through 529 Processing helix chain 'A' and resid 546 through 550 Processing helix chain 'A' and resid 596 through 600 removed outlier: 4.112A pdb=" N LEU A 600 " --> pdb=" O ALA A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 812 Processing helix chain 'A' and resid 814 through 822 Processing helix chain 'A' and resid 825 through 853 removed outlier: 4.271A pdb=" N SER A 829 " --> pdb=" O GLY A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 898 Processing helix chain 'A' and resid 907 through 914 Processing helix chain 'A' and resid 925 through 930 removed outlier: 3.837A pdb=" N VAL A 929 " --> pdb=" O CYS A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 959 removed outlier: 3.561A pdb=" N ALA A 946 " --> pdb=" O ASN A 942 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA A 956 " --> pdb=" O LEU A 952 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLY A 957 " --> pdb=" O GLY A 953 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLY A 959 " --> pdb=" O ILE A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 983 Processing helix chain 'A' and resid 986 through 993 removed outlier: 3.676A pdb=" N LEU A 990 " --> pdb=" O THR A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1008 removed outlier: 3.586A pdb=" N ILE A 997 " --> pdb=" O ASN A 993 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET A1008 " --> pdb=" O ALA A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1039 removed outlier: 3.906A pdb=" N LEU A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1058 Processing helix chain 'A' and resid 1059 through 1106 removed outlier: 3.788A pdb=" N ALA A1065 " --> pdb=" O PRO A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1200 No H-bonds generated for 'chain 'A' and resid 1198 through 1200' Processing helix chain 'B' and resid 36 through 41 removed outlier: 3.614A pdb=" N PHE B 40 " --> pdb=" O GLN B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'B' and resid 222 through 230 Processing helix chain 'B' and resid 303 through 307 removed outlier: 3.625A pdb=" N ARG B 307 " --> pdb=" O GLN B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 350 removed outlier: 3.630A pdb=" N GLN B 346 " --> pdb=" O ASN B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 390 Processing helix chain 'B' and resid 395 through 399 removed outlier: 3.842A pdb=" N PHE B 399 " --> pdb=" O VAL B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 415 removed outlier: 4.089A pdb=" N LEU B 414 " --> pdb=" O ASN B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 436 removed outlier: 3.929A pdb=" N SER B 435 " --> pdb=" O ALA B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 457 removed outlier: 4.066A pdb=" N MET B 452 " --> pdb=" O PRO B 449 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N SER B 454 " --> pdb=" O SER B 451 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER B 457 " --> pdb=" O SER B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 524 through 529 Processing helix chain 'B' and resid 546 through 550 Processing helix chain 'B' and resid 596 through 600 removed outlier: 4.113A pdb=" N LEU B 600 " --> pdb=" O ALA B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 805 through 812 Processing helix chain 'B' and resid 814 through 822 Processing helix chain 'B' and resid 825 through 853 removed outlier: 4.271A pdb=" N SER B 829 " --> pdb=" O GLY B 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 898 Processing helix chain 'B' and resid 907 through 914 Processing helix chain 'B' and resid 925 through 930 removed outlier: 3.837A pdb=" N VAL B 929 " --> pdb=" O CYS B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 940 through 959 removed outlier: 3.561A pdb=" N ALA B 946 " --> pdb=" O ASN B 942 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA B 956 " --> pdb=" O LEU B 952 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLY B 957 " --> pdb=" O GLY B 953 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLY B 959 " --> pdb=" O ILE B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 971 through 983 Processing helix chain 'B' and resid 986 through 993 removed outlier: 3.675A pdb=" N LEU B 990 " --> pdb=" O THR B 986 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1008 removed outlier: 3.586A pdb=" N ILE B 997 " --> pdb=" O ASN B 993 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET B1008 " --> pdb=" O ALA B1004 " (cutoff:3.500A) Processing helix chain 'B' and resid 1016 through 1039 removed outlier: 3.905A pdb=" N LEU B1036 " --> pdb=" O ALA B1032 " (cutoff:3.500A) Processing helix chain 'B' and resid 1050 through 1058 Processing helix chain 'B' and resid 1059 through 1106 removed outlier: 3.788A pdb=" N ALA B1065 " --> pdb=" O PRO B1061 " (cutoff:3.500A) Processing helix chain 'B' and resid 1198 through 1200 No H-bonds generated for 'chain 'B' and resid 1198 through 1200' Processing helix chain 'C' and resid 36 through 41 removed outlier: 3.614A pdb=" N PHE C 40 " --> pdb=" O GLN C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 53 Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 222 through 230 Processing helix chain 'C' and resid 303 through 307 removed outlier: 3.625A pdb=" N ARG C 307 " --> pdb=" O GLN C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 350 removed outlier: 3.630A pdb=" N GLN C 346 " --> pdb=" O ASN C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 390 Processing helix chain 'C' and resid 395 through 399 removed outlier: 3.842A pdb=" N PHE C 399 " --> pdb=" O VAL C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 415 removed outlier: 4.089A pdb=" N LEU C 414 " --> pdb=" O ASN C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 436 removed outlier: 3.930A pdb=" N SER C 435 " --> pdb=" O ALA C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 457 removed outlier: 4.065A pdb=" N MET C 452 " --> pdb=" O PRO C 449 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N SER C 454 " --> pdb=" O SER C 451 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER C 457 " --> pdb=" O SER C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 524 through 529 Processing helix chain 'C' and resid 546 through 550 Processing helix chain 'C' and resid 596 through 600 removed outlier: 4.112A pdb=" N LEU C 600 " --> pdb=" O ALA C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 805 through 812 Processing helix chain 'C' and resid 814 through 822 Processing helix chain 'C' and resid 825 through 853 removed outlier: 4.271A pdb=" N SER C 829 " --> pdb=" O GLY C 825 " (cutoff:3.500A) Processing helix chain 'C' and resid 888 through 898 Processing helix chain 'C' and resid 907 through 914 Processing helix chain 'C' and resid 925 through 930 removed outlier: 3.838A pdb=" N VAL C 929 " --> pdb=" O CYS C 925 " (cutoff:3.500A) Processing helix chain 'C' and resid 940 through 959 removed outlier: 3.560A pdb=" N ALA C 946 " --> pdb=" O ASN C 942 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA C 956 " --> pdb=" O LEU C 952 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLY C 957 " --> pdb=" O GLY C 953 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY C 959 " --> pdb=" O ILE C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 971 through 983 Processing helix chain 'C' and resid 986 through 993 removed outlier: 3.676A pdb=" N LEU C 990 " --> pdb=" O THR C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1008 removed outlier: 3.585A pdb=" N ILE C 997 " --> pdb=" O ASN C 993 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET C1008 " --> pdb=" O ALA C1004 " (cutoff:3.500A) Processing helix chain 'C' and resid 1016 through 1039 removed outlier: 3.905A pdb=" N LEU C1036 " --> pdb=" O ALA C1032 " (cutoff:3.500A) Processing helix chain 'C' and resid 1050 through 1058 Processing helix chain 'C' and resid 1059 through 1106 removed outlier: 3.788A pdb=" N ALA C1065 " --> pdb=" O PRO C1061 " (cutoff:3.500A) Processing helix chain 'C' and resid 1198 through 1200 No H-bonds generated for 'chain 'C' and resid 1198 through 1200' Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 75 removed outlier: 4.298A pdb=" N ARG A 335 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA3, first strand: chain 'A' and resid 88 through 89 removed outlier: 4.093A pdb=" N SER A 88 " --> pdb=" O HIS A 298 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE A 300 " --> pdb=" O SER A 88 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N THR A 206 " --> pdb=" O SER A 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 92 through 93 Processing sheet with id=AA5, first strand: chain 'A' and resid 110 through 111 Processing sheet with id=AA6, first strand: chain 'A' and resid 280 through 284 removed outlier: 5.141A pdb=" N GLN A 280 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N SER A 267 " --> pdb=" O GLN A 280 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 126 through 129 removed outlier: 4.286A pdb=" N SER A 126 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 154 through 155 Processing sheet with id=AA9, first strand: chain 'A' and resid 359 through 362 removed outlier: 4.129A pdb=" N TYR A 663 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N THR A 669 " --> pdb=" O ASP A 664 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 373 through 374 removed outlier: 6.605A pdb=" N VAL A 374 " --> pdb=" O SER A 607 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL A 639 " --> pdb=" O LEU A 651 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N VAL A 631 " --> pdb=" O VAL A 639 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 400 through 404 removed outlier: 6.709A pdb=" N THR A 483 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N VAL A 420 " --> pdb=" O THR A 483 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 513 through 515 removed outlier: 5.279A pdb=" N SER A 498 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL A 561 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ILE A 500 " --> pdb=" O SER A 559 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N SER A 559 " --> pdb=" O ILE A 500 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER A 504 " --> pdb=" O VAL A 555 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL A 555 " --> pdb=" O SER A 504 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP A 539 " --> pdb=" O GLY A 558 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 724 removed outlier: 6.949A pdb=" N VAL A 718 " --> pdb=" O LEU A 759 " (cutoff:3.500A) removed outlier: 8.926A pdb=" N SER A 761 " --> pdb=" O VAL A 718 " (cutoff:3.500A) removed outlier: 9.736A pdb=" N SER A 720 " --> pdb=" O SER A 761 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY A 732 " --> pdb=" O LEU A 735 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ALA A 737 " --> pdb=" O PRO A 730 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 778 through 795 removed outlier: 7.043A pdb=" N ASN A1145 " --> pdb=" O THR A 784 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N PHE A 786 " --> pdb=" O PRO A1143 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N PHE A 788 " --> pdb=" O TYR A1141 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N TYR A1141 " --> pdb=" O PHE A 788 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL A 790 " --> pdb=" O VAL A1139 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL A1139 " --> pdb=" O VAL A 790 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLN A 792 " --> pdb=" O MET A1137 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N MET A1137 " --> pdb=" O GLN A 792 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N TYR A 794 " --> pdb=" O TYR A1135 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N TYR A1135 " --> pdb=" O TYR A 794 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TYR A1135 " --> pdb=" O VAL A1127 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N VAL A1127 " --> pdb=" O TYR A1135 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N MET A1137 " --> pdb=" O SER A1125 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N SER A1125 " --> pdb=" O MET A1137 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL A1139 " --> pdb=" O ILE A1123 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR A1121 " --> pdb=" O TYR A1141 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 802 through 804 Processing sheet with id=AB7, first strand: chain 'A' and resid 1155 through 1157 removed outlier: 6.589A pdb=" N CYS A1156 " --> pdb=" O ILE A1214 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1164 through 1167 removed outlier: 3.901A pdb=" N CYS A1164 " --> pdb=" O VAL A1205 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1170 through 1173 Processing sheet with id=AC1, first strand: chain 'B' and resid 67 through 75 removed outlier: 4.299A pdb=" N ARG B 335 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AC3, first strand: chain 'B' and resid 88 through 89 removed outlier: 4.092A pdb=" N SER B 88 " --> pdb=" O HIS B 298 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE B 300 " --> pdb=" O SER B 88 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N THR B 206 " --> pdb=" O SER B 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 92 through 93 removed outlier: 3.500A pdb=" N THR B 96 " --> pdb=" O THR B 93 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 110 through 111 Processing sheet with id=AC6, first strand: chain 'B' and resid 280 through 284 removed outlier: 5.141A pdb=" N GLN B 280 " --> pdb=" O SER B 267 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N SER B 267 " --> pdb=" O GLN B 280 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 126 through 129 removed outlier: 4.285A pdb=" N SER B 126 " --> pdb=" O ILE B 140 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 154 through 155 Processing sheet with id=AC9, first strand: chain 'B' and resid 359 through 362 removed outlier: 4.129A pdb=" N TYR B 663 " --> pdb=" O GLY B 359 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N THR B 669 " --> pdb=" O ASP B 664 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 373 through 374 removed outlier: 6.605A pdb=" N VAL B 374 " --> pdb=" O SER B 607 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL B 639 " --> pdb=" O LEU B 651 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N VAL B 631 " --> pdb=" O VAL B 639 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 400 through 404 removed outlier: 6.710A pdb=" N THR B 483 " --> pdb=" O VAL B 420 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N VAL B 420 " --> pdb=" O THR B 483 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 513 through 515 removed outlier: 5.279A pdb=" N SER B 498 " --> pdb=" O VAL B 561 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL B 561 " --> pdb=" O SER B 498 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ILE B 500 " --> pdb=" O SER B 559 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N SER B 559 " --> pdb=" O ILE B 500 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER B 504 " --> pdb=" O VAL B 555 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL B 555 " --> pdb=" O SER B 504 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP B 539 " --> pdb=" O GLY B 558 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 718 through 724 removed outlier: 6.950A pdb=" N VAL B 718 " --> pdb=" O LEU B 759 " (cutoff:3.500A) removed outlier: 8.926A pdb=" N SER B 761 " --> pdb=" O VAL B 718 " (cutoff:3.500A) removed outlier: 9.735A pdb=" N SER B 720 " --> pdb=" O SER B 761 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY B 732 " --> pdb=" O LEU B 735 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ALA B 737 " --> pdb=" O PRO B 730 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 778 through 795 removed outlier: 7.044A pdb=" N ASN B1145 " --> pdb=" O THR B 784 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N PHE B 786 " --> pdb=" O PRO B1143 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N PHE B 788 " --> pdb=" O TYR B1141 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N TYR B1141 " --> pdb=" O PHE B 788 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL B 790 " --> pdb=" O VAL B1139 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL B1139 " --> pdb=" O VAL B 790 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLN B 792 " --> pdb=" O MET B1137 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N MET B1137 " --> pdb=" O GLN B 792 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N TYR B 794 " --> pdb=" O TYR B1135 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N TYR B1135 " --> pdb=" O TYR B 794 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TYR B1135 " --> pdb=" O VAL B1127 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N VAL B1127 " --> pdb=" O TYR B1135 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N MET B1137 " --> pdb=" O SER B1125 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N SER B1125 " --> pdb=" O MET B1137 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL B1139 " --> pdb=" O ILE B1123 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR B1121 " --> pdb=" O TYR B1141 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 802 through 804 Processing sheet with id=AD7, first strand: chain 'B' and resid 1155 through 1157 removed outlier: 6.589A pdb=" N CYS B1156 " --> pdb=" O ILE B1214 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'B' and resid 1164 through 1167 removed outlier: 3.900A pdb=" N CYS B1164 " --> pdb=" O VAL B1205 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1170 through 1173 Processing sheet with id=AE1, first strand: chain 'C' and resid 67 through 75 removed outlier: 4.298A pdb=" N ARG C 335 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 85 through 86 Processing sheet with id=AE3, first strand: chain 'C' and resid 88 through 89 removed outlier: 4.093A pdb=" N SER C 88 " --> pdb=" O HIS C 298 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE C 300 " --> pdb=" O SER C 88 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N THR C 206 " --> pdb=" O SER C 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 92 through 93 Processing sheet with id=AE5, first strand: chain 'C' and resid 110 through 111 Processing sheet with id=AE6, first strand: chain 'C' and resid 280 through 284 removed outlier: 5.141A pdb=" N GLN C 280 " --> pdb=" O SER C 267 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N SER C 267 " --> pdb=" O GLN C 280 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 126 through 129 removed outlier: 4.286A pdb=" N SER C 126 " --> pdb=" O ILE C 140 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 154 through 155 Processing sheet with id=AE9, first strand: chain 'C' and resid 359 through 362 removed outlier: 4.129A pdb=" N TYR C 663 " --> pdb=" O GLY C 359 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N THR C 669 " --> pdb=" O ASP C 664 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 373 through 374 removed outlier: 6.605A pdb=" N VAL C 374 " --> pdb=" O SER C 607 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL C 639 " --> pdb=" O LEU C 651 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N VAL C 631 " --> pdb=" O VAL C 639 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 400 through 404 removed outlier: 6.709A pdb=" N THR C 483 " --> pdb=" O VAL C 420 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N VAL C 420 " --> pdb=" O THR C 483 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 513 through 515 removed outlier: 5.280A pdb=" N SER C 498 " --> pdb=" O VAL C 561 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL C 561 " --> pdb=" O SER C 498 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ILE C 500 " --> pdb=" O SER C 559 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N SER C 559 " --> pdb=" O ILE C 500 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER C 504 " --> pdb=" O VAL C 555 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL C 555 " --> pdb=" O SER C 504 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP C 539 " --> pdb=" O GLY C 558 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 718 through 724 removed outlier: 6.949A pdb=" N VAL C 718 " --> pdb=" O LEU C 759 " (cutoff:3.500A) removed outlier: 8.926A pdb=" N SER C 761 " --> pdb=" O VAL C 718 " (cutoff:3.500A) removed outlier: 9.735A pdb=" N SER C 720 " --> pdb=" O SER C 761 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY C 732 " --> pdb=" O LEU C 735 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ALA C 737 " --> pdb=" O PRO C 730 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 778 through 795 removed outlier: 7.043A pdb=" N ASN C1145 " --> pdb=" O THR C 784 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N PHE C 786 " --> pdb=" O PRO C1143 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N PHE C 788 " --> pdb=" O TYR C1141 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N TYR C1141 " --> pdb=" O PHE C 788 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL C 790 " --> pdb=" O VAL C1139 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL C1139 " --> pdb=" O VAL C 790 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLN C 792 " --> pdb=" O MET C1137 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N MET C1137 " --> pdb=" O GLN C 792 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N TYR C 794 " --> pdb=" O TYR C1135 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N TYR C1135 " --> pdb=" O TYR C 794 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TYR C1135 " --> pdb=" O VAL C1127 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N VAL C1127 " --> pdb=" O TYR C1135 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N MET C1137 " --> pdb=" O SER C1125 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N SER C1125 " --> pdb=" O MET C1137 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL C1139 " --> pdb=" O ILE C1123 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR C1121 " --> pdb=" O TYR C1141 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 802 through 804 Processing sheet with id=AF7, first strand: chain 'C' and resid 1155 through 1157 removed outlier: 6.588A pdb=" N CYS C1156 " --> pdb=" O ILE C1214 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'C' and resid 1164 through 1167 removed outlier: 3.901A pdb=" N CYS C1164 " --> pdb=" O VAL C1205 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 1170 through 1173 977 hydrogen bonds defined for protein. 2574 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.20 Time building geometry restraints manager: 12.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4785 1.32 - 1.45: 8076 1.45 - 1.58: 15477 1.58 - 1.70: 0 1.70 - 1.83: 204 Bond restraints: 28542 Sorted by residual: bond pdb=" CA GLU C 944 " pdb=" C GLU C 944 " ideal model delta sigma weight residual 1.523 1.413 0.110 1.30e-02 5.92e+03 7.16e+01 bond pdb=" CA GLU B 944 " pdb=" C GLU B 944 " ideal model delta sigma weight residual 1.523 1.414 0.110 1.30e-02 5.92e+03 7.10e+01 bond pdb=" CA GLU A 944 " pdb=" C GLU A 944 " ideal model delta sigma weight residual 1.523 1.414 0.109 1.30e-02 5.92e+03 7.06e+01 bond pdb=" CA ASP A 940 " pdb=" C ASP A 940 " ideal model delta sigma weight residual 1.526 1.433 0.093 1.37e-02 5.33e+03 4.64e+01 bond pdb=" CA ASP C 940 " pdb=" C ASP C 940 " ideal model delta sigma weight residual 1.526 1.434 0.092 1.37e-02 5.33e+03 4.53e+01 ... (remaining 28537 not shown) Histogram of bond angle deviations from ideal: 97.78 - 105.02: 522 105.02 - 112.27: 14125 112.27 - 119.51: 9252 119.51 - 126.75: 14639 126.75 - 133.99: 291 Bond angle restraints: 38829 Sorted by residual: angle pdb=" N GLU A 944 " pdb=" CA GLU A 944 " pdb=" C GLU A 944 " ideal model delta sigma weight residual 111.28 97.78 13.50 1.09e+00 8.42e-01 1.53e+02 angle pdb=" N GLU C 944 " pdb=" CA GLU C 944 " pdb=" C GLU C 944 " ideal model delta sigma weight residual 111.28 97.80 13.48 1.09e+00 8.42e-01 1.53e+02 angle pdb=" N GLU B 944 " pdb=" CA GLU B 944 " pdb=" C GLU B 944 " ideal model delta sigma weight residual 111.28 97.83 13.45 1.09e+00 8.42e-01 1.52e+02 angle pdb=" CA ARG C 221 " pdb=" CB ARG C 221 " pdb=" CG ARG C 221 " ideal model delta sigma weight residual 114.10 124.28 -10.18 2.00e+00 2.50e-01 2.59e+01 angle pdb=" CA ARG B 221 " pdb=" CB ARG B 221 " pdb=" CG ARG B 221 " ideal model delta sigma weight residual 114.10 124.27 -10.17 2.00e+00 2.50e-01 2.58e+01 ... (remaining 38824 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.45: 16528 24.45 - 48.91: 935 48.91 - 73.36: 189 73.36 - 97.81: 99 97.81 - 122.26: 78 Dihedral angle restraints: 17829 sinusoidal: 7638 harmonic: 10191 Sorted by residual: dihedral pdb=" CB CYS A 811 " pdb=" SG CYS A 811 " pdb=" SG CYS A 817 " pdb=" CB CYS A 817 " ideal model delta sinusoidal sigma weight residual -86.00 -160.04 74.04 1 1.00e+01 1.00e-02 6.96e+01 dihedral pdb=" CB CYS C 811 " pdb=" SG CYS C 811 " pdb=" SG CYS C 817 " pdb=" CB CYS C 817 " ideal model delta sinusoidal sigma weight residual -86.00 -160.04 74.04 1 1.00e+01 1.00e-02 6.96e+01 dihedral pdb=" CB CYS B 811 " pdb=" SG CYS B 811 " pdb=" SG CYS B 817 " pdb=" CB CYS B 817 " ideal model delta sinusoidal sigma weight residual -86.00 -160.02 74.02 1 1.00e+01 1.00e-02 6.96e+01 ... (remaining 17826 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.158: 4449 0.158 - 0.316: 72 0.316 - 0.474: 3 0.474 - 0.632: 0 0.632 - 0.790: 3 Chirality restraints: 4527 Sorted by residual: chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN C 222 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.61 -0.79 2.00e-01 2.50e+01 1.56e+01 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 222 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.61 -0.79 2.00e-01 2.50e+01 1.56e+01 chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN B 222 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.61 -0.79 2.00e-01 2.50e+01 1.56e+01 ... (remaining 4524 not shown) Planarity restraints: 4989 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 222 " 0.057 2.00e-02 2.50e+03 5.51e-02 3.79e+01 pdb=" CG ASN C 222 " -0.057 2.00e-02 2.50e+03 pdb=" OD1 ASN C 222 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN C 222 " -0.069 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " 0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 222 " 0.057 2.00e-02 2.50e+03 5.50e-02 3.79e+01 pdb=" CG ASN A 222 " -0.057 2.00e-02 2.50e+03 pdb=" OD1 ASN A 222 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 222 " -0.069 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " 0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 222 " -0.057 2.00e-02 2.50e+03 5.47e-02 3.74e+01 pdb=" CG ASN B 222 " 0.057 2.00e-02 2.50e+03 pdb=" OD1 ASN B 222 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN B 222 " 0.069 2.00e-02 2.50e+03 pdb=" C1 NAG M 1 " -0.061 2.00e-02 2.50e+03 ... (remaining 4986 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 3288 2.75 - 3.29: 26923 3.29 - 3.83: 47926 3.83 - 4.36: 52962 4.36 - 4.90: 90940 Nonbonded interactions: 222039 Sorted by model distance: nonbonded pdb=" OG SER A 268 " pdb=" O ASP A 272 " model vdw 2.218 2.440 nonbonded pdb=" OG SER C 268 " pdb=" O ASP C 272 " model vdw 2.218 2.440 nonbonded pdb=" OG SER B 268 " pdb=" O ASP B 272 " model vdw 2.218 2.440 nonbonded pdb=" OD1 ASN C 421 " pdb=" OG1 THR C 483 " model vdw 2.243 2.440 nonbonded pdb=" OD1 ASN B 421 " pdb=" OG1 THR B 483 " model vdw 2.243 2.440 ... (remaining 222034 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'Q' } ncs_group { reference = chain 'E' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.320 Check model and map are aligned: 0.390 Set scattering table: 0.260 Process input model: 76.440 Find NCS groups from input model: 1.680 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 28542 Z= 0.347 Angle : 0.831 13.495 38829 Z= 0.441 Chirality : 0.059 0.790 4527 Planarity : 0.006 0.091 4950 Dihedral : 18.729 122.263 11175 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.14 % Favored : 94.69 % Rotamer: Outliers : 0.30 % Allowed : 0.56 % Favored : 99.14 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.14), residues: 3462 helix: 0.29 (0.19), residues: 681 sheet: 0.42 (0.20), residues: 678 loop : -1.09 (0.13), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B1184 HIS 0.003 0.001 HIS A 836 PHE 0.026 0.002 PHE A 239 TYR 0.020 0.002 TYR A1141 ARG 0.011 0.001 ARG A 822 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 238 time to evaluate : 3.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8948 (tmm) cc_final: 0.8482 (tmm) REVERT: A 576 GLN cc_start: 0.9089 (mp10) cc_final: 0.8827 (mp10) REVERT: A 938 LEU cc_start: 0.8098 (tp) cc_final: 0.7887 (tp) REVERT: B 84 MET cc_start: 0.8842 (tmm) cc_final: 0.8538 (tmm) REVERT: B 940 ASP cc_start: 0.6930 (m-30) cc_final: 0.6304 (m-30) REVERT: B 1053 ASP cc_start: 0.9039 (m-30) cc_final: 0.8412 (t70) REVERT: C 940 ASP cc_start: 0.7479 (m-30) cc_final: 0.7012 (m-30) outliers start: 9 outliers final: 2 residues processed: 241 average time/residue: 0.3307 time to fit residues: 135.8420 Evaluate side-chains 177 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 175 time to evaluate : 3.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 293 optimal weight: 3.9990 chunk 263 optimal weight: 8.9990 chunk 146 optimal weight: 7.9990 chunk 90 optimal weight: 8.9990 chunk 177 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 chunk 272 optimal weight: 8.9990 chunk 105 optimal weight: 7.9990 chunk 165 optimal weight: 7.9990 chunk 203 optimal weight: 7.9990 chunk 316 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN ** A 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 ASN ** A 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN ** B 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 800 GLN B 812 ASN ** B 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 ASN C 812 ASN ** C 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 28542 Z= 0.459 Angle : 0.763 10.267 38829 Z= 0.388 Chirality : 0.050 0.308 4527 Planarity : 0.006 0.062 4950 Dihedral : 15.319 110.798 5085 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.07 % Favored : 93.85 % Rotamer: Outliers : 0.03 % Allowed : 5.85 % Favored : 94.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.14), residues: 3462 helix: 0.67 (0.20), residues: 699 sheet: -0.17 (0.19), residues: 696 loop : -1.00 (0.13), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 960 HIS 0.008 0.002 HIS B 264 PHE 0.024 0.002 PHE B 778 TYR 0.021 0.002 TYR C1211 ARG 0.005 0.001 ARG B 979 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 210 time to evaluate : 3.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 ASP cc_start: 0.8325 (t0) cc_final: 0.8112 (t0) REVERT: A 757 MET cc_start: 0.8353 (mpp) cc_final: 0.8029 (mpp) REVERT: B 240 MET cc_start: 0.8229 (tpp) cc_final: 0.7911 (tpp) REVERT: B 940 ASP cc_start: 0.7122 (m-30) cc_final: 0.6031 (m-30) REVERT: B 1008 MET cc_start: 0.7503 (ppp) cc_final: 0.7040 (ppp) REVERT: B 1053 ASP cc_start: 0.9075 (m-30) cc_final: 0.8707 (t70) REVERT: B 1148 GLU cc_start: 0.8241 (mm-30) cc_final: 0.8040 (pm20) REVERT: B 1189 SER cc_start: 0.9115 (m) cc_final: 0.8796 (p) REVERT: C 240 MET cc_start: 0.8253 (tpp) cc_final: 0.7572 (tpp) REVERT: C 326 ASP cc_start: 0.8295 (t0) cc_final: 0.8052 (t0) REVERT: C 940 ASP cc_start: 0.7014 (m-30) cc_final: 0.6202 (m-30) REVERT: C 1053 ASP cc_start: 0.8896 (m-30) cc_final: 0.8482 (t70) outliers start: 1 outliers final: 1 residues processed: 211 average time/residue: 0.3776 time to fit residues: 134.2820 Evaluate side-chains 165 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 164 time to evaluate : 3.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 175 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 263 optimal weight: 6.9990 chunk 215 optimal weight: 8.9990 chunk 87 optimal weight: 0.6980 chunk 316 optimal weight: 7.9990 chunk 342 optimal weight: 6.9990 chunk 281 optimal weight: 30.0000 chunk 313 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 253 optimal weight: 10.0000 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 114 ASN ** A 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 GLN A 812 ASN ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN B 114 ASN ** B 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 516 GLN B 519 ASN ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN C 114 ASN ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 516 GLN C 519 ASN ** C 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 28542 Z= 0.336 Angle : 0.658 9.434 38829 Z= 0.331 Chirality : 0.047 0.327 4527 Planarity : 0.005 0.060 4950 Dihedral : 14.553 113.844 5085 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.14), residues: 3462 helix: 0.95 (0.20), residues: 693 sheet: -0.31 (0.19), residues: 696 loop : -1.03 (0.13), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 253 HIS 0.004 0.001 HIS A 836 PHE 0.022 0.002 PHE B 778 TYR 0.019 0.002 TYR B1153 ARG 0.002 0.000 ARG B 887 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 3.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.9085 (tmm) cc_final: 0.8721 (tmm) REVERT: A 326 ASP cc_start: 0.8354 (t0) cc_final: 0.8110 (t0) REVERT: A 757 MET cc_start: 0.8174 (mpp) cc_final: 0.7668 (mpp) REVERT: A 1053 ASP cc_start: 0.9055 (m-30) cc_final: 0.8607 (t70) REVERT: B 105 TYR cc_start: 0.8845 (m-80) cc_final: 0.8505 (m-80) REVERT: B 208 HIS cc_start: 0.7635 (t70) cc_final: 0.6566 (t-90) REVERT: B 213 ASP cc_start: 0.7788 (m-30) cc_final: 0.6314 (t70) REVERT: B 326 ASP cc_start: 0.8377 (t0) cc_final: 0.8165 (t0) REVERT: B 943 MET cc_start: 0.8173 (tpt) cc_final: 0.7925 (tpt) REVERT: B 1053 ASP cc_start: 0.9028 (m-30) cc_final: 0.8672 (t70) REVERT: B 1189 SER cc_start: 0.9127 (m) cc_final: 0.8746 (p) REVERT: C 326 ASP cc_start: 0.8310 (t0) cc_final: 0.8046 (t0) REVERT: C 944 GLU cc_start: 0.8313 (mm-30) cc_final: 0.8079 (mm-30) REVERT: C 1053 ASP cc_start: 0.8887 (m-30) cc_final: 0.8509 (t70) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.3392 time to fit residues: 125.4072 Evaluate side-chains 167 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 3.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 312 optimal weight: 6.9990 chunk 238 optimal weight: 0.1980 chunk 164 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 chunk 151 optimal weight: 20.0000 chunk 212 optimal weight: 0.8980 chunk 317 optimal weight: 0.4980 chunk 336 optimal weight: 3.9990 chunk 165 optimal weight: 7.9990 chunk 301 optimal weight: 10.0000 chunk 90 optimal weight: 0.5980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN ** A 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 ASN ** B 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 ASN ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28542 Z= 0.167 Angle : 0.585 9.499 38829 Z= 0.287 Chirality : 0.045 0.303 4527 Planarity : 0.004 0.062 4950 Dihedral : 13.421 115.833 5085 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.14), residues: 3462 helix: 1.38 (0.21), residues: 681 sheet: -0.27 (0.18), residues: 774 loop : -0.87 (0.14), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 253 HIS 0.006 0.001 HIS A 766 PHE 0.015 0.001 PHE C 266 TYR 0.029 0.001 TYR C 105 ARG 0.002 0.000 ARG B 221 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 3.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.9049 (tmm) cc_final: 0.8626 (tmm) REVERT: A 153 VAL cc_start: 0.6890 (t) cc_final: 0.6681 (m) REVERT: A 433 ILE cc_start: 0.9089 (pt) cc_final: 0.8844 (pt) REVERT: A 757 MET cc_start: 0.8166 (mpp) cc_final: 0.7507 (mpp) REVERT: A 1053 ASP cc_start: 0.9001 (m-30) cc_final: 0.8617 (t70) REVERT: B 84 MET cc_start: 0.8888 (tmm) cc_final: 0.8579 (tmm) REVERT: B 208 HIS cc_start: 0.7472 (t70) cc_final: 0.6544 (t70) REVERT: B 213 ASP cc_start: 0.7754 (m-30) cc_final: 0.6418 (t70) REVERT: B 240 MET cc_start: 0.7855 (tpt) cc_final: 0.7583 (tpp) REVERT: B 326 ASP cc_start: 0.8231 (t0) cc_final: 0.8000 (t0) REVERT: B 433 ILE cc_start: 0.9191 (pt) cc_final: 0.8972 (pt) REVERT: B 794 TYR cc_start: 0.8634 (t80) cc_final: 0.8277 (t80) REVERT: B 1053 ASP cc_start: 0.9024 (m-30) cc_final: 0.8706 (t70) REVERT: B 1189 SER cc_start: 0.9020 (m) cc_final: 0.8646 (p) REVERT: C 433 ILE cc_start: 0.9202 (pt) cc_final: 0.8988 (pt) REVERT: C 943 MET cc_start: 0.8130 (ttt) cc_final: 0.7265 (ttt) REVERT: C 944 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7966 (mm-30) REVERT: C 1053 ASP cc_start: 0.8894 (m-30) cc_final: 0.8525 (t70) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.3590 time to fit residues: 149.8864 Evaluate side-chains 176 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 3.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 280 optimal weight: 8.9990 chunk 190 optimal weight: 0.7980 chunk 4 optimal weight: 7.9990 chunk 250 optimal weight: 10.0000 chunk 138 optimal weight: 4.9990 chunk 287 optimal weight: 40.0000 chunk 232 optimal weight: 50.0000 chunk 0 optimal weight: 50.0000 chunk 171 optimal weight: 8.9990 chunk 301 optimal weight: 8.9990 chunk 84 optimal weight: 4.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 796 GLN A 842 GLN ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 HIS ** B 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 ASN ** B 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 796 GLN B 842 GLN ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 796 GLN C 800 GLN C 842 GLN ** C 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 28542 Z= 0.422 Angle : 0.725 9.830 38829 Z= 0.365 Chirality : 0.047 0.248 4527 Planarity : 0.005 0.059 4950 Dihedral : 13.623 116.706 5085 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.14), residues: 3462 helix: 0.91 (0.20), residues: 681 sheet: -0.66 (0.18), residues: 738 loop : -1.05 (0.13), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 960 HIS 0.007 0.002 HIS B 264 PHE 0.025 0.002 PHE A 778 TYR 0.023 0.002 TYR A1153 ARG 0.005 0.001 ARG B 979 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 3.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 296 ILE cc_start: 0.9193 (mp) cc_final: 0.8989 (mp) REVERT: A 326 ASP cc_start: 0.8367 (t0) cc_final: 0.8076 (t0) REVERT: A 757 MET cc_start: 0.8215 (mpp) cc_final: 0.7786 (mpp) REVERT: A 1008 MET cc_start: 0.7361 (ppp) cc_final: 0.6351 (ppp) REVERT: A 1053 ASP cc_start: 0.9060 (m-30) cc_final: 0.8605 (t70) REVERT: B 84 MET cc_start: 0.8956 (tmm) cc_final: 0.8610 (tmm) REVERT: B 326 ASP cc_start: 0.8394 (t0) cc_final: 0.8193 (t0) REVERT: B 1053 ASP cc_start: 0.9078 (m-30) cc_final: 0.8746 (t70) REVERT: C 296 ILE cc_start: 0.9207 (mp) cc_final: 0.9005 (mp) REVERT: C 326 ASP cc_start: 0.8459 (t0) cc_final: 0.8118 (t0) REVERT: C 731 LEU cc_start: 0.8608 (tp) cc_final: 0.8391 (tp) REVERT: C 944 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8053 (mm-30) REVERT: C 1053 ASP cc_start: 0.8863 (m-30) cc_final: 0.8458 (t70) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.3439 time to fit residues: 125.6581 Evaluate side-chains 159 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 3.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 113 optimal weight: 0.9990 chunk 302 optimal weight: 0.5980 chunk 66 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 336 optimal weight: 3.9990 chunk 279 optimal weight: 0.9980 chunk 155 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 111 optimal weight: 0.0040 chunk 176 optimal weight: 8.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN ** A 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 436 ASN ** A 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 ASN ** B 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 ASN ** B 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 ASN ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 ASN ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 436 ASN ** C 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 28542 Z= 0.162 Angle : 0.603 9.499 38829 Z= 0.294 Chirality : 0.045 0.239 4527 Planarity : 0.004 0.061 4950 Dihedral : 12.646 118.396 5085 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.14), residues: 3462 helix: 1.54 (0.21), residues: 663 sheet: -0.26 (0.18), residues: 759 loop : -0.89 (0.14), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 253 HIS 0.007 0.001 HIS A1122 PHE 0.034 0.001 PHE B 164 TYR 0.027 0.001 TYR B 105 ARG 0.003 0.000 ARG C 887 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 3.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.9053 (tmm) cc_final: 0.8689 (tmm) REVERT: A 266 PHE cc_start: 0.8022 (m-80) cc_final: 0.7500 (m-10) REVERT: A 757 MET cc_start: 0.8188 (mpp) cc_final: 0.7514 (mpp) REVERT: A 1053 ASP cc_start: 0.9045 (m-30) cc_final: 0.8602 (t70) REVERT: B 84 MET cc_start: 0.8958 (tmm) cc_final: 0.8601 (tmm) REVERT: B 940 ASP cc_start: 0.6958 (m-30) cc_final: 0.6265 (m-30) REVERT: B 1053 ASP cc_start: 0.9003 (m-30) cc_final: 0.8703 (t70) REVERT: B 1189 SER cc_start: 0.9048 (m) cc_final: 0.8664 (p) REVERT: C 326 ASP cc_start: 0.8288 (t0) cc_final: 0.7999 (t0) REVERT: C 731 LEU cc_start: 0.8454 (tp) cc_final: 0.8228 (tp) REVERT: C 1053 ASP cc_start: 0.8867 (m-30) cc_final: 0.8519 (t70) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.3453 time to fit residues: 142.5639 Evaluate side-chains 172 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 3.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 324 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 191 optimal weight: 2.9990 chunk 245 optimal weight: 7.9990 chunk 190 optimal weight: 3.9990 chunk 283 optimal weight: 40.0000 chunk 188 optimal weight: 9.9990 chunk 335 optimal weight: 9.9990 chunk 209 optimal weight: 9.9990 chunk 204 optimal weight: 0.9980 chunk 154 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 ASN B 208 HIS ** B 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 ASN ** B 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 ASN ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 28542 Z= 0.279 Angle : 0.639 16.944 38829 Z= 0.314 Chirality : 0.045 0.231 4527 Planarity : 0.004 0.062 4950 Dihedral : 12.482 118.886 5085 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.14), residues: 3462 helix: 1.25 (0.21), residues: 684 sheet: -0.43 (0.18), residues: 759 loop : -0.91 (0.14), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 960 HIS 0.006 0.001 HIS B 208 PHE 0.024 0.001 PHE B 164 TYR 0.017 0.001 TYR A1153 ARG 0.003 0.000 ARG B 979 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 2.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.9104 (tmm) cc_final: 0.8762 (tmm) REVERT: A 326 ASP cc_start: 0.8340 (t0) cc_final: 0.8108 (t0) REVERT: A 757 MET cc_start: 0.8105 (mpp) cc_final: 0.7435 (mpp) REVERT: A 1008 MET cc_start: 0.7244 (ppp) cc_final: 0.6112 (ppp) REVERT: A 1053 ASP cc_start: 0.9055 (m-30) cc_final: 0.8604 (t70) REVERT: B 84 MET cc_start: 0.9023 (tmm) cc_final: 0.8682 (tmm) REVERT: B 1053 ASP cc_start: 0.9041 (m-30) cc_final: 0.8697 (t70) REVERT: C 326 ASP cc_start: 0.8344 (t0) cc_final: 0.8028 (t0) REVERT: C 1053 ASP cc_start: 0.8913 (m-30) cc_final: 0.8518 (t70) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.3342 time to fit residues: 127.2573 Evaluate side-chains 164 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 3.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 207 optimal weight: 2.9990 chunk 133 optimal weight: 8.9990 chunk 200 optimal weight: 0.6980 chunk 101 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 213 optimal weight: 4.9990 chunk 228 optimal weight: 2.9990 chunk 165 optimal weight: 20.0000 chunk 31 optimal weight: 0.7980 chunk 263 optimal weight: 4.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN ** A 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 ASN ** B 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 ASN ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28542 Z= 0.223 Angle : 0.616 9.422 38829 Z= 0.301 Chirality : 0.045 0.222 4527 Planarity : 0.004 0.062 4950 Dihedral : 12.125 119.328 5085 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.14), residues: 3462 helix: 1.30 (0.21), residues: 684 sheet: -0.41 (0.18), residues: 732 loop : -0.87 (0.14), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 253 HIS 0.003 0.001 HIS B1122 PHE 0.021 0.001 PHE B 164 TYR 0.020 0.001 TYR C 105 ARG 0.003 0.000 ARG C 887 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 3.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 TYR cc_start: 0.7369 (m-80) cc_final: 0.7050 (m-80) REVERT: A 84 MET cc_start: 0.9100 (tmm) cc_final: 0.8734 (tmm) REVERT: A 160 LYS cc_start: 0.8075 (mttp) cc_final: 0.7831 (mtmt) REVERT: A 326 ASP cc_start: 0.8297 (t0) cc_final: 0.8067 (t0) REVERT: A 757 MET cc_start: 0.8093 (mpp) cc_final: 0.7426 (mpp) REVERT: A 1008 MET cc_start: 0.7207 (ppp) cc_final: 0.6091 (ppp) REVERT: A 1053 ASP cc_start: 0.9062 (m-30) cc_final: 0.8629 (t70) REVERT: B 84 MET cc_start: 0.9011 (tmm) cc_final: 0.8679 (tmm) REVERT: B 1008 MET cc_start: 0.7317 (ppp) cc_final: 0.6664 (ppp) REVERT: B 1053 ASP cc_start: 0.9021 (m-30) cc_final: 0.8625 (t70) REVERT: C 326 ASP cc_start: 0.8307 (t0) cc_final: 0.8011 (t0) REVERT: C 1053 ASP cc_start: 0.8855 (m-30) cc_final: 0.8501 (t70) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.3305 time to fit residues: 127.1021 Evaluate side-chains 163 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 3.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 305 optimal weight: 0.8980 chunk 321 optimal weight: 0.9990 chunk 293 optimal weight: 4.9990 chunk 312 optimal weight: 8.9990 chunk 188 optimal weight: 10.0000 chunk 136 optimal weight: 0.0060 chunk 245 optimal weight: 20.0000 chunk 95 optimal weight: 10.0000 chunk 282 optimal weight: 6.9990 chunk 295 optimal weight: 3.9990 chunk 311 optimal weight: 1.9990 overall best weight: 1.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN ** A 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 ASN ** B 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 ASN ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28542 Z= 0.181 Angle : 0.607 13.217 38829 Z= 0.293 Chirality : 0.044 0.228 4527 Planarity : 0.004 0.061 4950 Dihedral : 11.641 119.168 5085 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.14), residues: 3462 helix: 1.42 (0.21), residues: 684 sheet: -0.42 (0.19), residues: 726 loop : -0.82 (0.14), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 253 HIS 0.005 0.001 HIS C1122 PHE 0.020 0.001 PHE B 164 TYR 0.020 0.001 TYR C 105 ARG 0.002 0.000 ARG C 887 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 3.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 TYR cc_start: 0.7307 (m-80) cc_final: 0.7006 (m-80) REVERT: A 84 MET cc_start: 0.9091 (tmm) cc_final: 0.8710 (tmm) REVERT: A 160 LYS cc_start: 0.8074 (mttp) cc_final: 0.7848 (mtmt) REVERT: A 326 ASP cc_start: 0.8225 (t0) cc_final: 0.8020 (t0) REVERT: A 757 MET cc_start: 0.8047 (mpp) cc_final: 0.7369 (mpp) REVERT: A 1008 MET cc_start: 0.7137 (ppp) cc_final: 0.6118 (ppp) REVERT: A 1053 ASP cc_start: 0.9037 (m-30) cc_final: 0.8601 (t70) REVERT: B 84 MET cc_start: 0.9005 (tmm) cc_final: 0.8646 (tmm) REVERT: B 208 HIS cc_start: 0.7134 (t-90) cc_final: 0.6190 (t-170) REVERT: B 213 ASP cc_start: 0.7753 (m-30) cc_final: 0.6314 (t70) REVERT: B 326 ASP cc_start: 0.8322 (t0) cc_final: 0.8105 (t0) REVERT: B 1008 MET cc_start: 0.7242 (ppp) cc_final: 0.6634 (ppp) REVERT: B 1053 ASP cc_start: 0.9009 (m-30) cc_final: 0.8619 (t70) REVERT: B 1148 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7879 (mm-30) REVERT: C 326 ASP cc_start: 0.8234 (t0) cc_final: 0.7995 (t0) REVERT: C 927 GLN cc_start: 0.6710 (pp30) cc_final: 0.6390 (pp30) REVERT: C 938 LEU cc_start: 0.8650 (tp) cc_final: 0.8370 (tt) REVERT: C 1053 ASP cc_start: 0.8889 (m-30) cc_final: 0.8518 (t70) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.3531 time to fit residues: 138.3600 Evaluate side-chains 175 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 3.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 205 optimal weight: 5.9990 chunk 330 optimal weight: 6.9990 chunk 201 optimal weight: 7.9990 chunk 156 optimal weight: 10.0000 chunk 229 optimal weight: 2.9990 chunk 346 optimal weight: 8.9990 chunk 319 optimal weight: 7.9990 chunk 276 optimal weight: 0.7980 chunk 28 optimal weight: 9.9990 chunk 213 optimal weight: 9.9990 chunk 169 optimal weight: 30.0000 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 28542 Z= 0.378 Angle : 0.719 12.435 38829 Z= 0.359 Chirality : 0.047 0.257 4527 Planarity : 0.005 0.060 4950 Dihedral : 11.792 117.971 5085 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.14), residues: 3462 helix: 1.02 (0.21), residues: 684 sheet: -0.69 (0.18), residues: 717 loop : -1.00 (0.14), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 960 HIS 0.005 0.002 HIS B 81 PHE 0.032 0.002 PHE B 778 TYR 0.028 0.002 TYR C 105 ARG 0.004 0.001 ARG A 221 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 3.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 TYR cc_start: 0.7573 (m-80) cc_final: 0.7246 (m-80) REVERT: A 84 MET cc_start: 0.9185 (tmm) cc_final: 0.8805 (tmm) REVERT: A 148 MET cc_start: 0.7294 (tmm) cc_final: 0.6934 (tmm) REVERT: A 326 ASP cc_start: 0.8357 (t0) cc_final: 0.8076 (t0) REVERT: A 757 MET cc_start: 0.8144 (mpp) cc_final: 0.7543 (mpp) REVERT: A 1008 MET cc_start: 0.7350 (ppp) cc_final: 0.6317 (ppp) REVERT: A 1053 ASP cc_start: 0.9043 (m-30) cc_final: 0.8635 (t70) REVERT: B 84 MET cc_start: 0.9043 (tmm) cc_final: 0.8697 (tmm) REVERT: B 266 PHE cc_start: 0.8321 (m-10) cc_final: 0.7673 (m-80) REVERT: B 326 ASP cc_start: 0.8359 (t0) cc_final: 0.8158 (t0) REVERT: B 938 LEU cc_start: 0.8527 (tp) cc_final: 0.8312 (tp) REVERT: B 1008 MET cc_start: 0.7489 (ppp) cc_final: 0.6923 (ppp) REVERT: B 1053 ASP cc_start: 0.9022 (m-30) cc_final: 0.8591 (t70) REVERT: C 326 ASP cc_start: 0.8421 (t0) cc_final: 0.8076 (t0) REVERT: C 938 LEU cc_start: 0.8770 (tp) cc_final: 0.8569 (tp) REVERT: C 1008 MET cc_start: 0.7643 (ppp) cc_final: 0.6594 (ppp) REVERT: C 1053 ASP cc_start: 0.8927 (m-30) cc_final: 0.8502 (t70) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.3467 time to fit residues: 126.9736 Evaluate side-chains 160 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 3.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 219 optimal weight: 2.9990 chunk 294 optimal weight: 9.9990 chunk 84 optimal weight: 0.9990 chunk 254 optimal weight: 10.0000 chunk 40 optimal weight: 20.0000 chunk 76 optimal weight: 1.9990 chunk 276 optimal weight: 0.0170 chunk 115 optimal weight: 7.9990 chunk 283 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 overall best weight: 1.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN ** A 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 ASN ** B 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 ASN ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.097308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.072021 restraints weight = 101133.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.073867 restraints weight = 56532.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.075109 restraints weight = 39708.231| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28542 Z= 0.184 Angle : 0.618 13.857 38829 Z= 0.300 Chirality : 0.045 0.234 4527 Planarity : 0.004 0.061 4950 Dihedral : 10.991 117.779 5085 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.14), residues: 3462 helix: 1.17 (0.21), residues: 702 sheet: -0.54 (0.19), residues: 744 loop : -0.91 (0.14), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 253 HIS 0.006 0.001 HIS C1122 PHE 0.019 0.001 PHE B 164 TYR 0.020 0.001 TYR B 105 ARG 0.003 0.000 ARG A1057 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4292.93 seconds wall clock time: 81 minutes 9.97 seconds (4869.97 seconds total)